Manure substitution counteracts mineral nitrogen-driven erosion of the phoD guild and supports phosphorus mobilisation in acidified paddy soil

Maintaining microbially mediated phosphorus mobilisation under intensive nitrogen fertilisation is difficult in acidified paddy soils. Using a decade-long field experiment in a rice–oilseed rape rotation, we compared an ordered manure-substitution series, in which manure input increased while mineral nitrogen input decreased, with a mineral nitrogen dose gradient. Increasing mineral nitrogen input was associated with lower diversity and absolute abundance of the phoD-harbouring bacterial guild and a marked shift in community composition. Across the manure-substitution series, soil pH increased from 5.94 to 6.62, potential alkaline phosphatase activity increased by up to 158%, and Olsen-extractable phosphorus increased by up to 182%. The diversity, composition, and absolute abundance of the phoD guild changed progressively across the same series. Distance-based redundancy analysis identified soil pH as the strongest measured marginal correlate of community composition, whereas variation partitioning indicated that the effects of pH, carbon, and phosphorus were largely shared. An exploratory structural equation model was consistent with conditional associations of both community composition and absolute gene abundance with alkaline phosphatase activity, which was in turn associated with Olsen-extractable phosphorus. The highest observed means for gene abundance, grain yield, and grain phosphorus removal occurred in the intermediate manure treatment, whereas treatment-level copper and zinc concentrations increased towards the highest-manure treatment. Together, these findings indicate that manure substitution can counteract mineral nitrogen-associated deterioration of the phoD guild and support microbial phosphorus mobilisation, although the agronomic and metal responses require confirmation across sites and seasons.